org.forester.surfacing

Class DomainCountsDifferenceUtil

java.lang.Object

org.forester.surfacing.DomainCountsDifferenceUtil

public final class DomainCountsDifferenceUtil
extends Object

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static class	DomainCountsDifferenceUtil.COPY_CALCULATION_MODE

Constructor Summary

Constructors

Constructor and Description
DomainCountsDifferenceUtil()

Method Summary

Modifier and Type

Method and Description

static void

calculateCopyNumberDifferences(List<GenomeWideCombinableDomains> genomes, SortedMap<Species,List<Protein>> protein_lists_per_species, List<String> high_copy_base_species, List<String> high_copy_target_species, List<String> low_copy_species, int min_diff, Double factor, File plain_output_dom, File html_output_dom, File html_output_dc, Map<String,List<GoId>> domain_id_to_go_ids_map, Map<GoId,GoTerm> go_id_to_term_map, File all_domains_go_ids_out_dom, File passing_domains_go_ids_out_dom, File proteins_file_base)

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

DomainCountsDifferenceUtil

public DomainCountsDifferenceUtil()

Method Detail

calculateCopyNumberDifferences

public static void calculateCopyNumberDifferences(List<GenomeWideCombinableDomains> genomes,
                                                  SortedMap<Species,List<Protein>> protein_lists_per_species,
                                                  List<String> high_copy_base_species,
                                                  List<String> high_copy_target_species,
                                                  List<String> low_copy_species,
                                                  int min_diff,
                                                  Double factor,
                                                  File plain_output_dom,
                                                  File html_output_dom,
                                                  File html_output_dc,
                                                  Map<String,List<GoId>> domain_id_to_go_ids_map,
                                                  Map<GoId,GoTerm> go_id_to_term_map,
                                                  File all_domains_go_ids_out_dom,
                                                  File passing_domains_go_ids_out_dom,
                                                  File proteins_file_base)
                                           throws IOException

Throws:

IOException